Schools are reporting large and unexplained overpayments in holiday pay in Novopay's end-of-year cycle.

An email was sent to all schools yesterday confirming all 92,000 staff had been paid in the end-of-year pay cycle. But new problems had been found, and about 5000 non-teaching staff would get their holiday pay a day late, it said.

The New Zealand Educational Institute (NZEI) says the error-riddled Novopay system is making school staff "seriously stressed" as they try to complete end-of-year payments.

Wellington East Girls' College acting principal Anne Greenaway said she had already found 13 errors in the school's expense report, mainly holiday pay overpayments to relief workers or support staff. "[Novopay] doesn't seem to be able to manage those sorts of complications in the payroll system."

A "classic example" was a young man, who did just 30 hours casual labour on the school grounds in July, being paid 32 hours of holiday pay.

"He was not working here for that time," Ms Greenaway said. "It suddenly appeared on our report randomly. It's some of those strange things that just seem to appear."

Reports were usually 15 pages long, but the latest required staff to scrutinise 38 pages of payroll data.

"We don't have the trust in the system any more, so we do have to check it. And there were at least 13 errors that we know of.

"It's been very frustrating and it's taken hours of work."

Education Ministry chief information officer Leanne Gibson said the ministry and contractor Talent2 were working hard to ensure holiday payments went through as smoothly as possible, but regretted the delay in holiday payment to some staff.

Fortnightly pay for permanent teaching staff that would have fallen during Christmas week has been brought forward to December 21.

NZEI national president Ian Leckie said Novopay was not improving, despite ministry claims.

"The Ministry of Education has unleashed a catastrophe and we don't believe this is something that can be sorted this side of Christmas."